One example of microscopes capable of acquiring a three-dimensional structure of a specimen to be observed is a microscope using stochastic optical reconstruction microscopy (hereinafter referred to as “STORM”) (see, for example, U.S. Patent Application Publication No. 2008/0182335). STORM is used to observe a specimen with fluorescent substances. For example, STORM activates a fluorescent substance at low density and causes only the activated fluorescent substance to emit light by irradiation of excitation light, thereby acquiring a fluorescence image in which images of fluorescence are sparsely distributed. In the fluorescence image, the images of fluorescence are individually separated, and the centroid positions of the individual images are able to be determined by Gaussian fitting or the like. STORM generates (constructs) a high-resolution image by arranging point images at the centroid positions of a large number of fluorescent substances obtained from a large number of fluorescence images. For example, the structure of a specimen is able to be acquired three-dimensionally by determining the position of a fluorescent substance for each of a plurality of layers of the specimen and integrating the positions of fluorescent substances for the layers.
As described above, it is desired to match information among a plurality of layers in acquiring three-dimensional information on a specimen for each of the layers.